While tremendous progress has been made in genetic definition and biological treatments for rheumatoid arthritis (RA), there remains a lack of fundamental knowledge about the pathogenesis and heterogeneity of this disorder. Recent technological developments allow for precise molecular analysis of disease tissues down to the single cell level. We propose to interrogate circulating immune cells and synovial tissue cells to identify the molecular and cellular correlates between systemic immune cell diversity, synovial pathology and clinical phenotypes. In Specific aim 1 (phase 0), we will optimize processes for the preparation and storage of synovial tissue and peripheral blood leukocyte samples in order to support a variety of advanced analytic techniques. These include single cell RNA seq of synovial tissue cells, epigenetic studies (ATAC-Seq), CyTOF mass cytometry for high-dimensional analysis of cellular phenotypes, and RNA seq analysis of at least 12 peripheral blood leukoctye subsets. We will also support development and feasibility studies of novel technologies for in situ molecular and cellular analysis of histological sections of synovial tissu. In addition, we will develop synovial cell lines to enable detailed study of synovial cell biology.In Specific Aim 2 (phase 1), we will enroll 30 subjects with rheumatoid arthritis for study of blood and synovial tissue using the technologies developed and validated in phase 0. A systems level analysis of these data will drive the selection of specific assays to be utilized in a larger patiet cohort. In Specific Aim 3 (phase 2), we will carry out an observational cohort study of 250 early RA patients enrolled over a three year period with analysis of both synovial tissue and peripheral blood leukocytes. We will employ a set of focused assays that emerge from the studies in Phase 0 and 1. The disease course, therapy and response to therapy will be documented in all patients. We will address the following hypotheses: 1) multiparameter analysis of synovial tissue can define subsets of disease with distinct clinical features or outcomes; 2) analysis of peripheral blood cell subsets with high dimensional molecular and cellular data, can identify correlates for these disease subsets; 3) useful parameters can be developed that can identify, as well as predict, therapeutic response.